Sunday, November 23, 2014

Autosomal Pedigree Creator

A tool that automatically creates a pedigree tree based on segment matches from a set of autosomal files. This tool will also let you know how a segment match of an unrelated genetic match is related and through whom. Supports FTDNA, 23andMe and Ancestry files.

Prerequisites:
Usage:
  1. Rename autosomal filenames to have meaningful names like their actual names or Father, Mother etc. No numbers just alphabets.
  2. Copy all the renamed files to a folder.
  3. Browse and select the that folder.
  4. Pedigree created. Enjoy!
Note: To get best results, make sure you have the kit along with the parents’ kits as well. If you don’t have any parents and you got a blank pedigree or you got some individuals omitted, try dump all option.

Screenshots:
Tool in action

Generated Output


Download Autosomal Pedigree Creator.zip (810 KB)

Documentation: Autosomal Pedigree Creator.pdf (1.04 MB) (Online Version)

Source Code at GitHub.

License: MIT License.

Change Log
Version 1.5
  • Supports Ancestry files.
Version 1.4
  • Allows alphanumeric names for kits.
Version 1.3
  • Minor bug-fix to provide more accurate pedigree.
Version 1.2
  • Dump-all option for remotely/unrelated autosomal files.
Version 1.1
  • Minor bug-fix.
Version 1.0
  • Initial release.

Wednesday, November 19, 2014

Ancient Ancestry

Ancient Ancestry is a tool to compare an autosomal DNA with already triangulated ancient DNA segments. The tool will also provide a hierarchical view of how each segment flows through ancients. and allows you to export into an excel friendly format for further analysis. The tool supports FTDNA, 23andMe and Ancestry with build 37 autosomal files.

Prerequisites:
Usage: Open an autosomal file and the tool will automatically plot the matching segments.

Screenshots:




Download Ancient Ancestry.exe (4.89 MB).

Source Code at GitHub.

License: MIT License.

Change Log
Version 1.0
  • Initial release.

Ancient Hungarian Neolithic genome - NE1

The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. The authors had analysed a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. I converted the raw data of NE1 from Polgár-Ferenci-hát site in Hungary into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and uploaded to GEDmatch as kit# F999937.

Download: 
Reference:
Cristina Gamba, Eppie R. Jones, Matthew D. Teasdale, Russell L. McLaughlin, Gloria Gonzalez-Fortes, Valeria Mattiangeli, László Domboróczki, Ivett Kővári, Ildikó Pap, Alexandra Anders, Alasdair Whittle, János Dani, Pál Raczky, Thomas F. G. Higham, Michael Hofreiter, Daniel G. Bradley & Ron Pinhasi "Genome flux and stasis in a five millennium transect of European prehistory" doi:10.1038/ncomms6257.

Data Used

Saturday, November 15, 2014

Neanderthal Vi33.26 DNA

Authors had provided Neanderthal genomes with their publications. I converted the raw data of Vi33.26 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.

Download: 
Reference:
Green, Richard E., Johannes Krause, Adrian W. Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson et al. "A draft sequence of the Neandertal genome." science 328, no. 5979 (2010): 710-722.

Data Used

Neanderthal Vi33.25 DNA

Authors had provided Neanderthal genomes with their publications. I converted the raw data of Vi33.25 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.

Download: 
Reference:
Green, Richard E., Johannes Krause, Adrian W. Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson et al. "A draft sequence of the Neandertal genome." science 328, no. 5979 (2010): 710-722.

Data Used